Strain identifier
BacDive ID: 453
Type strain:
Species: Paraglaciecola polaris
Strain history: CIP <- 2004, S. Van Trappen, Ghent Univ., Ghent, Belgium <- T.L. Tan, Wegener Inst.: strain ARK 150
NCBI tax ID(s): 1129793 (strain), 222814 (species)
General
@ref: 6448
BacDive-ID: 453
DSM-Number: 16457
keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative, motile, rod-shaped
description: Paraglaciecola polaris DSM 16457 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from sea water .
NCBI tax id
NCBI tax id | Matching level |
---|---|
1129793 | strain |
222814 | species |
strain history
@ref | history |
---|---|
6448 | <- S. Van Trappen; ARK 150 <- T. L. Tan |
121925 | CIP <- 2004, S. Van Trappen, Ghent Univ., Ghent, Belgium <- T.L. Tan, Wegener Inst.: strain ARK 150 |
doi: 10.13145/bacdive453.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Alteromonadales
- family: Alteromonadaceae
- genus: Paraglaciecola
- species: Paraglaciecola polaris
- full scientific name: Paraglaciecola polaris (Van Trappen et al. 2004) Shivaji and Reddy 2014
synonyms
- @ref: 20215
- synonym: Glaciecola polaris
@ref: 6448
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Alteromonadales
family: Alteromonadaceae
genus: Paraglaciecola
species: Paraglaciecola polaris
full scientific name: Paraglaciecola polaris (Van Trappen et al. 2004) Shivaji and Reddy 2014
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31245 | negative | 2.5 µm | 0.4 µm | rod-shaped | yes | |
69480 | yes | 98.57 | ||||
69480 | negative | 99.998 | ||||
121925 | negative | rod-shaped | yes |
pigmentation
- @ref: 31245
- production: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6448 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water |
36580 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
121925 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6448 | positive | growth | 20 | psychrophilic |
31245 | positive | growth | 05-30 | |
31245 | positive | optimum | 17.5 | psychrophilic |
36580 | positive | growth | 20 | psychrophilic |
121925 | positive | growth | 5-25 | psychrophilic |
121925 | no | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 31245
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.966 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31245 | NaCl | positive | growth | <10 % |
31245 | NaCl | positive | optimum | 5 % |
121925 | NaCl | positive | growth | 2-6 % |
121925 | NaCl | no | growth | 0 % |
121925 | NaCl | no | growth | 8 % |
121925 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31245 | 30089 | acetate | + | carbon source |
31245 | 16449 | alanine | + | carbon source |
31245 | 18403 | L-arabitol | + | carbon source |
31245 | 17057 | cellobiose | + | carbon source |
31245 | 23652 | dextrin | + | carbon source |
31245 | 28757 | fructose | + | carbon source |
31245 | 28260 | galactose | + | carbon source |
31245 | 17234 | glucose | + | carbon source |
31245 | 29987 | glutamate | + | carbon source |
31245 | 28087 | glycogen | + | carbon source |
31245 | 17716 | lactose | + | carbon source |
31245 | 25017 | leucine | + | carbon source |
31245 | 17306 | maltose | + | carbon source |
31245 | 29864 | mannitol | + | carbon source |
31245 | 37684 | mannose | + | carbon source |
31245 | 28053 | melibiose | + | carbon source |
31245 | 37657 | methyl D-glucoside | + | carbon source |
31245 | 51850 | methyl pyruvate | + | carbon source |
31245 | 17272 | propionate | + | carbon source |
31245 | 16634 | raffinose | + | carbon source |
31245 | 17814 | salicin | + | carbon source |
31245 | 17992 | sucrose | + | carbon source |
31245 | 27082 | trehalose | + | carbon source |
31245 | 53423 | tween 40 | + | carbon source |
31245 | 53426 | tween 80 | + | carbon source |
31245 | 4853 | esculin | + | hydrolysis |
121925 | 4853 | esculin | - | hydrolysis |
121925 | 17632 | nitrate | - | reduction |
121925 | 16301 | nitrite | - | reduction |
121925 | 132112 | sodium thiosulfate | - | builds gas from |
metabolite production
- @ref: 121925
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
31245 | acid phosphatase | + | 3.1.3.2 |
31245 | alkaline phosphatase | + | 3.1.3.1 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | + | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
121925 | oxidase | + | |
121925 | beta-galactosidase | + | 3.2.1.23 |
121925 | alcohol dehydrogenase | - | 1.1.1.1 |
121925 | gelatinase | +/- | |
121925 | amylase | + | |
121925 | caseinase | + | 3.4.21.50 |
121925 | catalase | + | 1.11.1.6 |
121925 | tween esterase | + | |
121925 | lecithinase | + | |
121925 | lipase | + | |
121925 | lysine decarboxylase | - | 4.1.1.18 |
121925 | ornithine decarboxylase | - | 4.1.1.17 |
121925 | protease | + | |
121925 | tryptophan deaminase | - | |
121925 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121925 | + | + | + | + | + | + | + | - | - | - | + | + | + | - | - | - | + | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121925 | + | - | + | + | - | - | - | + | - | + | - | + | + | - | - | + | + | + | + | - | - | + | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | isolation date |
---|---|---|---|---|
6448 | sea water (25m depth) | Arctic Ocean | ||
121925 | Environment, Arctic sea water | Western Greenland Sea | 1997 |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_6761.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_98;96_345;97_456;98_525;99_6761&stattab=map
- Last taxonomy: Paraglaciecola polaris
- 16S sequence: AJ293820
- Sequence Identity:
- Total samples: 560
- soil counts: 1
- aquatic counts: 515
- animal counts: 41
- plant counts: 3
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
6448 | 1 | Risk group (German classification) |
121925 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 6448
- description: Glaciecola polaris 16S rRNA gene, type strain LMG 21857
- accession: AJ293820
- length: 1485
- database: ena
- NCBI tax ID: 222814
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Paraglaciecola polaris LMG 21857 | GCA_000315055 | contig | ncbi | 1129793 |
66792 | Glaciecola polaris LMG 21857 | 1129793.3 | wgs | patric | 1129793 |
66792 | Paraglaciecola polaris LMG 21857 | 2531839185 | draft | img | 1129793 |
GC content
- @ref: 31245
- GC-content: 44.2
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 89.678 | yes |
flagellated | yes | 83.662 | no |
gram-positive | no | 99.065 | yes |
anaerobic | no | 98.418 | yes |
halophile | yes | 64.193 | yes |
spore-forming | no | 97.369 | no |
glucose-util | yes | 93.676 | yes |
aerobic | yes | 87.863 | yes |
glucose-ferment | no | 79.274 | no |
thermophile | no | 99.696 | yes |
External links
@ref: 6448
culture collection no.: DSM 16457, CIP 108324, LMG 21857, ARK 150
straininfo link
- @ref: 70132
- straininfo: 28694
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15388742 | Glaciecola polaris sp. nov., a novel budding and prosthecate bacterium from the Arctic Ocean, and emended description of the genus Glaciecola. | Van Trappen S, Tan TL, Yang J, Mergaert J, Swings J | Int J Syst Evol Microbiol | 10.1099/ijs.0.63123-0 | 2004 | Alteromonadaceae/*classification/cytology/*isolation & purification/physiology, Antarctic Regions, Arctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis, Genes, rRNA, Microscopy, Electron, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Water Microbiology | Enzymology |
Phylogeny | 17473239 | Glaciecola agarilytica sp. nov., an agar-digesting marine bacterium from the East Sea, Korea. | Yong JJ, Park SJ, Kim HJ, Rhee SK | Int J Syst Evol Microbiol | 10.1099/ijs.0.64723-0 | 2007 | Agar/metabolism, Alteromonadaceae/*classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, Carbon/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA/genetics, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Temperature | Metabolism |
Metabolism | 28044272 | Gene cloning and expression of a glucoside 3-dehydrogenase from Sphingobacterium faecium ZJF-D6, and used it to produce N-p-nitrophenyl-3-ketovalidamine. | Zhang JF, Chen WQ, Chen H | World J Microbiol Biotechnol | 10.1007/s11274-016-2187-0 | 2017 | Bacterial Proteins/genetics/metabolism, Cloning, Molecular/*methods, Escherichia coli/genetics/metabolism, Galactosides/metabolism, Glucose Dehydrogenases/*genetics/*metabolism, Glucosides/metabolism, Hydrogen-Ion Concentration, Nitrophenols/*metabolism, Recombinant Proteins/metabolism, Sequence Homology, Amino Acid, Sphingobacterium/*enzymology/genetics, Substrate Specificity, Temperature | Enzymology |
Phylogeny | 32687464 | Paraglaciecola marina sp. nov., isolated from marine alga (Sargassum natans (L.) Gaillon). | Wang Y, Zhang Y, Liu T, Zhu X, Ma J, Su X, Kang J, Guo C | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004132 | 2020 | Alteromonadaceae/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sargassum/*microbiology, Seawater/microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
6448 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16457) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16457 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
31245 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 27568 | 28776041 | |
36580 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5934 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
68382 | Automatically annotated from API zym | |||||
69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
70132 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID28694.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121925 | Curators of the CIP | Collection of Institut Pasteur (CIP 108324) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108324 |